Members of the genus Bacteroides are by far the most abundant Gram-negative bacteria in the human gut microbiome. Recently we used mass spectrometry to examine the outer membrane (OM) proteome and secretome of one of the most commonly studied members of the Bacteroides genus, B. fragilis, grown under laboratory conditions. Although we did not identify any novel secretion pathways, we found that this organism uses a very different range of secretion strategies than Proteobacteria such as E. coli. B. fragilis lacks many of the pathways that are widespread among the Protebacteria (e.g., the type II, III and IV pathways) but produces multiple type I secretion systems simultaneously. B. fragilis also differs dramatically from Proteobacteria in that it produces a large number of lipoproteins that are exposed on the cell surface. The substrates of the type I pathways and the mechanism by which lipoproteins are transported across the OM are unknown. Interestingly, many of the proteins found in the secretome lack significant homology to proteins that are in the Genbank database and presumably have novel functions.